3 small holes on a sphere
I began with a cube that I subdivided smooth several times. And actually I ended up with a sort of UV Sphere. But anyway you could include the 6 holes part anywhere in a smoothed cube, as shown with the second sphere.

Note that in my modifiers stack I've used a Mirror, then a Subsurf, then a Shrinkrwrap.

The Target of the Shrinkwrap is also a smooth subdivided cube (or UV Sphere),as big as my object. It allows my object to nicely stick to a spherical shape. In my screenshot I made it invisible, of course.